Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

2017-04-11 Thread Jonathan Saboury 
Awesome! Thank you all so much!!!

Here is my implementation of the function for reference:

def passed_NA2SR(mol): #no atom shared by two small rings
rings = mol.GetRingInfo().AtomRings()
small_rings = []
for ring in rings:
if len(ring) < 5:
small_rings.append(ring)
small_ring_atoms = []
for small_ring in small_rings:
for ring_atom in small_ring:
if ring_atom in small_ring_atoms:
return False
else:
small_ring_atoms.append(ring_atom)
return True
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Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

2017-04-11 Thread Brian Kelley 
Peter, quite correct.

To do that, you'll need to do operations on the rings themselves:

>>> m = Chem.MolFromSmiles("C1CC12CCC2")

>>> list(m.GetRingInfo().AtomRings())

[(0, 1, 2), (3, 4, 5, 2)]

And set operations are probably your friend

>>> m = Chem.MolFromSmiles("C1CCC12CCC2")

>>> list(m.GetRingInfo().AtomRings())

[(0, 3, 2, 1), (4, 5, 6, 3)]

# get all 4 membered rings

>>> rings = [set(r) for r in m.GetRingInfo().AtomRings() if len(r) == 4]

# from the first ring, see if there are any intersections

>>> s = rings[0]

>>> for r in rings[1:]:

...   p = s.intersection(r)

...   if p: print p

...

set([3])

Cheers,
 Brian

On Tue, Apr 11, 2017 at 4:19 PM, Peter S. Shenkin  wrote:

> But Brian's solution won't help Jonathan find atoms that are in two
> three-membered or two four-membered rings, which I thought Jonathan also
> wanted, based on the wording of the original query.
>
> -P.
>
> On Tue, Apr 11, 2017 at 4:12 PM, Curt Fischer 
> wrote:
>
>> Brian's solution is obviously better (shorter, uses less functions) than
>> mine.  (Although mine assumes that you want atoms that are part of
>> _exactly_ two rings, not atoms that are part of _at least_ two rings as
>> Brian's does.  Probably Brian's solution is what you want but worth noting.)
>>
>> CF
>>
>> On Tue, Apr 11, 2017 at 1:03 PM, Brian Kelley 
>> wrote:
>>
>>> You are so close!
>>>
>>> >>> from rdkit import Chem
>>>
>>> >>> m = Chem.MolFromSmiles("C1CC12CCC2")
>>>
>>> >>> for atom in m.GetAtoms():
>>>
>>> ...   if atom.IsInRingSize(3) and atom.IsInRingSize(4): print
>>> atom.GetIdx()
>>>
>>> ...
>>>
>>> 2
>>>
>>> >>>
>>>
>>> Cheers,
>>>  Brian
>>>
>>> On Tue, Apr 11, 2017 at 1:38 PM, Jonathan Saboury 
>>> wrote:
>>>
 Hello All,

 I'm trying to make a function to check if a mol has an atom that is
 part of two small rings (3 or 4 atoms). Using GetRingInfo()/NumAtomRings()
 I can find out how many ring systems each atom is in, but not the details
 of the rings. atom.IsInRingSize(size) returns a bool so I couldn't use
 that. I'm using the python api.

 Any suggestions? Thanks!

 - Jonathan

 
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>>>
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>>
>> 
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>
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Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

2017-04-11 Thread Peter S. Shenkin 
But Brian's solution won't help Jonathan find atoms that are in two
three-membered or two four-membered rings, which I thought Jonathan also
wanted, based on the wording of the original query.

-P.

On Tue, Apr 11, 2017 at 4:12 PM, Curt Fischer 
wrote:

> Brian's solution is obviously better (shorter, uses less functions) than
> mine.  (Although mine assumes that you want atoms that are part of
> _exactly_ two rings, not atoms that are part of _at least_ two rings as
> Brian's does.  Probably Brian's solution is what you want but worth noting.)
>
> CF
>
> On Tue, Apr 11, 2017 at 1:03 PM, Brian Kelley 
> wrote:
>
>> You are so close!
>>
>> >>> from rdkit import Chem
>>
>> >>> m = Chem.MolFromSmiles("C1CC12CCC2")
>>
>> >>> for atom in m.GetAtoms():
>>
>> ...   if atom.IsInRingSize(3) and atom.IsInRingSize(4): print
>> atom.GetIdx()
>>
>> ...
>>
>> 2
>>
>> >>>
>>
>> Cheers,
>>  Brian
>>
>> On Tue, Apr 11, 2017 at 1:38 PM, Jonathan Saboury 
>> wrote:
>>
>>> Hello All,
>>>
>>> I'm trying to make a function to check if a mol has an atom that is part
>>> of two small rings (3 or 4 atoms). Using GetRingInfo()/NumAtomRings() I can
>>> find out how many ring systems each atom is in, but not the details of the
>>> rings. atom.IsInRingSize(size) returns a bool so I couldn't use that. I'm
>>> using the python api.
>>>
>>> Any suggestions? Thanks!
>>>
>>> - Jonathan
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>> 
>> --
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>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>
>>
>
> 
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Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

2017-04-11 Thread Curt Fischer 
Brian's solution is obviously better (shorter, uses less functions) than
mine.  (Although mine assumes that you want atoms that are part of
_exactly_ two rings, not atoms that are part of _at least_ two rings as
Brian's does.  Probably Brian's solution is what you want but worth noting.)

CF

On Tue, Apr 11, 2017 at 1:03 PM, Brian Kelley  wrote:

> You are so close!
>
> >>> from rdkit import Chem
>
> >>> m = Chem.MolFromSmiles("C1CC12CCC2")
>
> >>> for atom in m.GetAtoms():
>
> ...   if atom.IsInRingSize(3) and atom.IsInRingSize(4): print atom.GetIdx()
>
> ...
>
> 2
>
> >>>
>
> Cheers,
>  Brian
>
> On Tue, Apr 11, 2017 at 1:38 PM, Jonathan Saboury 
> wrote:
>
>> Hello All,
>>
>> I'm trying to make a function to check if a mol has an atom that is part
>> of two small rings (3 or 4 atoms). Using GetRingInfo()/NumAtomRings() I can
>> find out how many ring systems each atom is in, but not the details of the
>> rings. atom.IsInRingSize(size) returns a bool so I couldn't use that. I'm
>> using the python api.
>>
>> Any suggestions? Thanks!
>>
>> - Jonathan
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
> 
> --
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
>
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Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

2017-04-11 Thread Brian Kelley 
You are so close!

>>> from rdkit import Chem

>>> m = Chem.MolFromSmiles("C1CC12CCC2")

>>> for atom in m.GetAtoms():

...   if atom.IsInRingSize(3) and atom.IsInRingSize(4): print atom.GetIdx()

...

2

>>>

Cheers,
 Brian

On Tue, Apr 11, 2017 at 1:38 PM, Jonathan Saboury  wrote:

> Hello All,
>
> I'm trying to make a function to check if a mol has an atom that is part
> of two small rings (3 or 4 atoms). Using GetRingInfo()/NumAtomRings() I can
> find out how many ring systems each atom is in, but not the details of the
> rings. atom.IsInRingSize(size) returns a bool so I couldn't use that. I'm
> using the python api.
>
> Any suggestions? Thanks!
>
> - Jonathan
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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